LAMMPS (27 Mar 2011) # GayBerne ellipsoids in LJ background fluid units lj atom_style ellipsoid dimension 2 lattice sq 0.02 Lattice spacing in x,y,z = 7.07107 7.07107 7.07107 region box block 0 20 0 20 -0.5 0.5 create_box 2 box Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553) 2 by 2 by 1 processor grid create_atoms 1 box Created 400 atoms set group all type/fraction 2 0.1 95392 45 settings made for type/fraction set group all quat/random 18238 400 settings made for quat/random mass 1 1.0 mass 2 1.5 shape 1 1 1 1 shape 2 3 1 1 compute rot all temp/asphere group spheroid type 1 355 atoms in group spheroid variable dof equal count(spheroid)+2 compute_modify rot extra ${dof} compute_modify rot extra 357 velocity all create 2.4 87287 loop geom pair_style gayberne 1.0 3.0 1.0 4.0 pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5 pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0 pair_coeff 2 2 1.0 1.0 1 1 0.2 0 0 0 #pair_style resquared 4.0 #pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5 #pair_coeff 1 2 3.0 1 1 1 1 0 0 0 #pair_coeff 2 2 1.0 1 1 1 0.2 0 0 0 neighbor 0.8 bin thermo_style custom step c_rot epair etotal press vol thermo 100 timestep 0.002 dump 1 all custom 100 dump.ellipse.gayberne id type x y z quatw quati quatj quatk #dump 1 all custom 100 dump.ellipse.resquared # id type x y z quatw quati quatj quatk fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1 fix 2 all enforce2d compute_modify 1_temp extra ${dof} compute_modify 1_temp extra 357 # equilibrate to shrink box around dilute system run 2000 Memory usage per processor = 3.05653 Mbytes Step rot E_pair TotEng Press Volume 0 2.2718861 0 2.394 0.04788 20000 100 1.7443002 0 1.8380563 0.03576216 20558.672 200 2.2770454 0 2.3994366 0.046545139 20620.298 300 1.8573283 0 1.9571597 0.04240689 18460.771 400 2.1709963 -0.00050890768 2.2871782 0.066789189 13689.461 500 1.987484 -0.043660052 2.0342913 0.099199049 8475.4405 600 2.088535 -0.24318266 1.8270941 0.22391583 4674.8592 700 2.2604089 -0.73325761 1.481207 0.57184109 2507.095 800 1.8731398 -1.6161576 0.22080738 1.3049285 1420.4278 900 2.1404423 -3.0146759 -0.84039269 3.3566833 922.07169 1000 1.5927835 -4.5754144 -2.9697785 2.5493591 743.19289 1100 1.8380043 -4.8820159 -3.0604394 2.2950846 708.014 1200 2.05516 -4.5701279 -2.4718822 1.466469 753.52878 1300 2.0000364 -4.0755503 -2.031995 0.35675413 842.14053 1400 2.1055032 -3.7342781 -1.6632699 0.58193577 925.51606 1500 1.9241806 -3.582658 -1.639377 0.24973032 1006.7339 1600 2.125676 -3.4733166 -1.3572836 0.72069214 1061.1355 1700 1.8811354 -3.2933821 -1.4183258 0.59272021 1119.2646 1800 2.1014782 -3.1254259 -1.0248797 0.95254771 1162.1817 1900 1.8977855 -3.1905908 -1.2727444 0.73157369 1191.4876 2000 2.0794708 -3.253147 -1.2230906 0.4949131 1187.4615 Loop time of 0.471032 on 4 procs for 2000 steps with 400 atoms Pair time (%) = 0.233772 (49.6298) Neigh time (%) = 0.0046134 (0.979424) Comm time (%) = 0.0967541 (20.5409) Outpt time (%) = 0.0360661 (7.65683) Other time (%) = 0.0998262 (21.1931) Nlocal: 100 ave 113 max 79 min Histogram: 1 0 0 0 0 1 0 0 1 1 Nghost: 139.75 ave 151 max 132 min Histogram: 2 0 0 0 0 1 0 0 0 1 Neighs: 717 ave 880 max 487 min Histogram: 1 0 0 0 0 1 0 1 0 1 Total # of neighbors = 2868 Ave neighs/atom = 7.17 Neighbor list builds = 138 Dangerous builds = 80 # run dynamics on dense system unfix 1 fix 1 all nve/asphere run 2000 Memory usage per processor = 3.05737 Mbytes Step rot E_pair TotEng Press Volume 2000 2.0794708 -3.253147 -1.2230906 0.4949131 1187.4615 2100 2.0350673 -3.2084761 -1.1823685 0.33981977 1187.4615 2200 1.9674878 -3.1385618 -1.1467435 1.1720135 1187.4615 2300 2.0160348 -3.1912829 -1.1652126 0.98222401 1187.4615 2400 2.1323062 -3.3152814 -1.1669962 0.7609989 1187.4615 2500 2.0866913 -3.2692051 -1.1766059 0.67971628 1187.4615 2600 2.0982825 -3.2774432 -1.1869919 0.90454622 1187.4615 2700 2.0482776 -3.2229453 -1.192888 0.69426696 1187.4615 2800 1.9676403 -3.1400511 -1.1685935 0.75777885 1187.4615 2900 2.0421568 -3.2182511 -1.1867014 0.79371143 1187.4615 3000 2.1074324 -3.2870215 -1.201353 0.18881974 1187.4615 3100 2.0468246 -3.2229216 -1.1821138 0.70504941 1187.4615 3200 2.1169492 -3.2986856 -1.1589351 0.51871921 1187.4615 3300 2.1536413 -3.3397682 -1.180639 0.44887653 1187.4615 3400 2.0978165 -3.280631 -1.1610415 0.75128792 1187.4615 3500 2.0587882 -3.2398235 -1.1433609 0.80394373 1187.4615 3600 2.0255166 -3.2025649 -1.1720208 0.54192507 1187.4615 3700 2.0154027 -3.1893307 -1.1657023 0.28402513 1187.4615 3800 1.9277814 -3.0960105 -1.1854881 0.77670745 1187.4615 3900 2.0112013 -3.1831546 -1.1850665 0.67676688 1187.4615 4000 2.0284348 -3.2011574 -1.1772834 0.41947147 1187.4615 Loop time of 0.539757 on 4 procs for 2000 steps with 400 atoms Pair time (%) = 0.289897 (53.7087) Neigh time (%) = 0.00209838 (0.388764) Comm time (%) = 0.148968 (27.599) Outpt time (%) = 0.0367653 (6.81144) Other time (%) = 0.0620289 (11.492) Nlocal: 100 ave 119 max 68 min Histogram: 1 0 0 0 0 0 1 0 1 1 Nghost: 137.25 ave 151 max 128 min Histogram: 2 0 0 0 0 1 0 0 0 1 Neighs: 735.25 ave 965 max 403 min Histogram: 1 0 0 0 0 1 0 0 1 1 Total # of neighbors = 2941 Ave neighs/atom = 7.3525 Neighbor list builds = 46 Dangerous builds = 0